The Anomaly
by Sorrowful Skies
Summary: One day, she found that...place. Now it's up to them to stop it from entering their world. Matrix Cross-over. Possible Yuri.
1. Enter The Matrix

He ran. The agents were behind him, gaining. He knew that if they caught him, he would have to stand and fight. He wasn't prepared to do that. Not now. Especially with Agent Smith. No, he had to run.

He leaped over a fence, rolling to lessen the impact. He quickly got to his feet and kept running. The Agents behind him quickly broke the fence apart and chased him. He jumped on top of a dustbin and leaped up a wall. He grabbed a ledge and pulled himself up, and continued to run. The Agents behind him were close now, almost on the building to. He ran to the edge of the building and looked down. It was a 4-storey drop, far to much to survive. The Agents were on the building now, almost within reach of him. He knew it was now or never.

Quickly, he span around. One of the Agents was charging at him, fist reared. Quickly, he hit him in the chest, and pivoted on his own axis, hitting the Agent in the face with a jaw-shattering Roundhouse kick. The Agent went flying, smashing into a power box. The other two Agents charged at him. He leaped over them, and spun around. He performed a sweep kick on one, then landed a punch on the other. The Agent stumbled backwards from the force of the punch, clutching his jaw. The other two Agents quickly ran to his side.

"The anomaly is proving to be a nuisance, Smith." said one.

"Yes, but he is still only human, Jones." said the one named Smith.

"Yes, should we engage?" asked another, looking at Smith.

"Only human, Brown." said Smith, adjusting his tie and sunglasses.

The Agents all wore business suits, with ties. They each had sunglasses on. Brown had his hair styled back, at a fairly short length. Smith had no hair, except a patch at the top on a few patches at the side. Jones had his hair parted at the sides. All of the Agent's hair were dark brown in colour.

He clenched his teeth. His trench coat blew in the wind. He was wearing a full black jumpsuit, with a black trench coat. His spiky blonde hair stood out in comparison to the dark atmosphere. His cerulean eyes were hidden behind sunglasses. He glared at the Agents behind them. Surveying the area, he saw a metal bar that could come in handy. Back flipping, he landed next to the bar.

"Engage." said Smith, and the Agents charged forward. Jones aimed a kick at his chest, which he quickly blocked. He twisted Jones' leg, and threw him away. He blocked a punch from Smith, and hit Brown back with a punch to the chest. Pivoting, he kicked Smith in the face, then jumped backwards, elbowing Brown into a charging Jones. Smith got up, and started throwing a flurry of punches at him.

He expertly blocked them all, then landed an uppercut into Smiths' jaw. He leg-swept Smith, then landed an axe kick into Smith's chest. Jones snuck up behind him, and caught him in a full nelson. Brown charged from the front, and gut punched him. He coughed up blood from the force of it. Brown smiled.

"Insignificant human. Your purpose ends here." he said, punching him again. The blonde kicked Brown away, then rolled forwards, throwing Jones off him. He got back up quickly, and sprinted towards the bar. Grasping it firmly, he levered it out of the concrete roof, and smashed the excess concrete on the floor. The Agents all got up, and glared at him angrily. The blonde spun the pole around, then let it rest on his shoulder, behind his neck. He beckoned the agents toward him with his left hand.

Enraged, Smith went first. He quickly smashed the pole into Smith's gut, then roundhouse kicked him away. He leapt towards Jones, smacking him square in the head with the pole. Brown leapt up, punching him across the face. He flew backwards, recovering rapidly. He landed gracefully, to meet a charging Brown. Smith charged him from behind, and Jones charged him from his left. He smirked.

"You're right, this is where it ends, Brown." He said. He smashed the pole into Brown, then spun around and jabbed into Smith's head. Pivoting, he punched Jones, then axe kicked him in the head. He spun a full 360 degrees and whacked Jones in the face with the metal pole, sending Jones flying off the roof. He picked up Brown by the cuff, and threw him off the roof to. Smith, seeing this, quickly got up and walked backwards.

"Believe me, filthy human, this is only the beginning." said the Agent, before leaping off the building. The blonde stared at the space where Smith was standing before for a while, before exhaling a large breath.

"And next time, I hope your ready." he said to the skies, before putting the pole down and walking towards the staircase.

She stared at the monitor, watching the green binary numbers go past. All seemed well, for now. He was doing his job well, and she needed him to stay like that. These people tending to their daily lives had no idea how hard this small group of talented people were working to keep life balanced. She took off her speaker and ear-piece, and let out a sigh. She put her pink hair in a pony tail, and fastened it with a hair clip.

Her name was Sakura Haruno. She wore a full white jumper, with white tracksuit bottoms and white boots, fastened with black laces. She had black gloves on. She sat in front of a large computer, with a massive keyboard, with certain keys in red and some in green, and some in black. There was one with a glass covering, and was gold in colour. Sakura pressed a few keys and got up. She walked over to a contraption that looked like something from a science-fiction movie.

It was a large sphere, made out of metal, with the front side cut off and a viewing glass there. Inside the sphere, there was an assortment of valves, tubes, pipes and wires, all connected to a metal oval, with 4 prongs inside it. It was on a metal stand. Outside the sphere, there was a melee of wires and pipes, connected to various machinery, notably the computer. It was Sakura's job to check all was well, which, for now, it was. She, and two colleagues, designed this entire intricate system. It took her 3 months to finish it, and she was very proud of her designs. She was constantly designing new ideas, tacking them up on walls wherever there was space. She sometimes worked well into the night, so she had a folding bed beside the computer, with a plastic bag containing bedspreads, duvets, and pillows. Sakura wouldn't let anybody really know about it, as she constantly complained about the constant diagnostics, and all the wires hat she constantly tripped over on, but she loved her invention. It was her metal hideout, her second home, her social area, and most of all, her way of proving she was useful.

Sakura's parents always hated her. She was hated because she was supposed to be married to a rich prince, which would bring the family riches and they could all live wonderful lives. Except Sakura. The prince was a snob, always commanding Sakura to do things for him, never showing any love to her. He simply used her as a slave. She would cry in the nights, into her pillow. She would write sorrowful things in her diary every day, and she would look out into the night sky, wondering how her life could be worse. During the day, while being a slave, she would dream about a man that would love her for who she was, and wouldn't treat her this bad. Finally, when the prince called her useless, and a particularly bad row, leading to Sakura running away. Immediately, the prince took away all the money that he gave the Haruno family, and ever since then, she was exiled from her family, never to come back.

The day she ran away was also the day she met him.

The sky had its familiar green tint, and the black clouds let loose rain onto the streets. He walked through puddles, and turned corners on a journey he knew well. He finally arrived at a seemingly ordinary road, and he stopped. Looking around, he made a hand sign and the brick wall beside him faded away, revealing the spherical machine. He walked into the room with the machine, and the brick wall reappeared, sealing him in. There was a computer terminal beside the machine, and he pressed a few buttons. The sphere opened, and he stepped inside. He closed the sphere, and pressed a red button. The sphere started to shake. He removed his glasses, and placed them in his pocket. He grasped a yellow lever, with a red handle, and pushed it forward. The sphere vibrated violently, and then he was gone in a flurry of green binary numbers.

Sakura sat back down on her comfy leather chair, holding a can of soda. She looked at the terminal, and noticed the green binary numbers rearranging themselves. She knew what this meant, and walked over to the sphere. It was vibrating violently. She closed her eyes, for a bright flash came out from the sphere. A flurry of green binary numbers entered the sphere, and the sphere stopped vibrating. Blonde stepped out. Sakura ran to him and embraced him. He hugged her back.

He looked at the pink haired woman in his arms. He loved to see her like this, in his arms. She stepped back, breaking the embrace.

"So, how did it go?" She asked.

"Fine, though I encountered the Agents on my way out. I seriously didn't feel like fighting them, but in the end, I had to." he replied.

"Oh, those guys." she said.

"Yeh. But, let's go now." he said. She gave him a smile, and they walked towards a heavy metal door. He opened it, and they walked up a few stairs into sunshine.

As they walked out, the green binary numbers started to alter very slightly. One of the numbers turned red…

Agent Smith faced Jones and Brown.

"We failed to terminate the anomaly this time." Said Jones.

" He is proving to be more skilled then we thought." said Brown.

"In the end though, he is still mortal. One decisive blow is all we need." stated Smith.

"We never get the chance to land that blow though." said Brown, clenching his teeth.

"Patience. We are superior beings, he will one day make an error. Then, we strike." said Smith.

"Yes, all we need is patience." said Jones.

"Mister Uzumaki will die, and then we will erase all other anomalies. From there, we enhance The Matrix, expand it, give it more purpose." Smith paused for a moment, looking at the other two Agents. "Then we gain more purpose."

"Yes. Our purpose outshines the inferior human's." Jones stated.

"We will encounter him again. When we do, we will initiate plan Alpha." Smith said.

Brown and Jones smiled. Smith placed his hands in his blazer pockets and walked away. Jones followed him shortly after, and Brown followed suit. He stopped momentarily though, to pick up a Golden Eagle. He fished his hand in his pocket, and pulled out a small metal device. He placed it on the barrel of gun, then place the gun in a shoulder holster inside his blazer pocket.

"Soon enough." He muttered to himself, walking towards the stairs. "Soon enough."


	2. The Past

He walked out onto the street with Sakura. The sun shone brightly over the tall buildings of the place he called home. The various dirt pathways were filled with the hustle and bustle of daily life, such as Shop-keepers pushing carts full of items that their shop was going to sell, ninjas leaping from roof to roof, People advertising their wares, and civilians trying to get around.

There was one prominent building that was much grander and taller then all the other buildings. It was in this building that the Supreme Ninja Leader, or Hokage, lead the village. This village was known as a ninja village, existing to protect the nation it works for, being the Fire Nation. Hokage literally translates to 'Fire Shadow'. The current Hokage, Tsunade Senju, was in her office, chugging down a bottle of sake.

She slammed the bottle on the table, and let out a big exhale of breath. She closed her eyes briefly, then opened them again.

"Man that was good." she said to herself.

Tsunade was renowned for her drinking and gambling (Or lack of) prowess. She wore a green jacket, with a traditional Japanese dress underneath. She had blonde hair, tied into two pony tails. She had hazel eyes, that were currently looking at a gargantuan pile of papers.

Tsunade sighed.

"Paperwork…" she mumbled to herself.

She began to stamp the papers, and sign them off, or leave comments, or just put a big line through them, when she spotted something particularly interesting.

"Naruto Uzumaki…" she read, looking at the name.

Her eyes darted around the page, scanning the contents. She put the paper down and looked at the 5 more pieces of paper. They were all about the same person…

The Hokage rubbed her forehead.

"You knucklehead…What have you done this time?"

"Naruto…" Sakura said, looking at the blonde named Naruto.

"Yes, Sakura-Chan?" he asked, while still looking ahead.

Sakura looked down at the floor a second.

"Can we sit on the Hokage monument? I want to talk to you." she asked.

Naruto raised an eyebrow, puzzled.

"Ok." he said, and he made a hand seal. A swirl of leaves engulfed them, and then they were gone.

The two reappeared on top of the Hokage monument. It was a massive mountain, with the faces of the five Hokages carved on it. This particular ninja village, known as Konohagakure no sato, roughly translated into The Village hidden in the leaves, had 5 Hokages. The reigning Hokage was the fifth.

"So…What did you want to ask me, Sakura?" Naruto started, sitting down.

Sakura followed suit.

"Well…Do you ever regret…That you met me?" she asked, looking at him.

"No! Of course not! Why?" he almost yelled, looking at Sakura.

"It's just…Everyday I keep sending you into that place, and you have to fight for your life, all because of me."

"No…I would do it any day…" He mentally added, "_For you._"

"Oh. Ok." Sakura said, a smile on her face.

"You know, I still remember the day we met." she said, smiling at Naruto.

"Yeh, I do to."

_-Flashback-_

Sakura slammed against a wall painfully. She had tears in her eyes, and multiple bruises on her arms. Her pink dress was ripped in several places, and her legs was badly bruised to. She clutched her left arm with her right firmly, and kept running. She could hear yelling behind her.

"Stop, slave! You belong to the Prince!"

"Halt!"

"Get back here!"

She had made up her mind, and wasn't going to give it up now. She turned another corner, into a well-lit ballroom. Three men, in massive green armour, with chain mail and halberds, stood at the exit on the other side of the ballroom. She spun around, seeing three more guards chasing her from this hallway. She ran into the centre of the ballroom. The guards closed in on her from both directions. She was trapped here. Her eyes darted around the room, looking for something that could help her.

The guards accelerated towards Sakura, and she quickly ran south, towards a bunch of tables. She jumped on top of one. There was a ledge, just low enough to reach. Sakura jumped up, her right hand firmly grabbing the ledge. She moved her battered left arm enough to grab the ledge. With a cry of pain, she pulled herself up and rolled onto the landing. The guards stopped and looked up. One, with a particularly pointy halberd, looked at the other 5.

"Send for the prince and reinforcements!" He barked at them, from behind his metal helmet.

"Yes sir!" They shouted in unison, giving a salute then running towards a hallway. The remaining g guard, who Sakura correctly assumed was the leader, growled at her.

"You may have escaped for now, girl, but you are the prince's slave! We will get you!" he yelled. Sakura got up and ran down the landing, into a hallway.

Sakura sprinted down the vast castle corridors, around seemingly endless corridors and rooms. Eventually, she came to a vast room, with a massive wooden door. She made it.

"_Yes!"_ she cheered inwardly. She ran to the door and pushed as hard as she could. The door opened very slightly, enough for Sakura to get through.

She emerged on the other side in a clearing, with forest all around. She dashed into the forest, and leaped over a tree root. She slowed down to a walk, and sat down by a stream for a rest. She washed her face, and her bruises, with the water. She let out a sigh of relief. She had finally escaped.

She rested her back against a tree, and drifted off into a blissful sleep…

Her sleep was broken when she felt big, metallic gloves grab her arms.

"I've found her!" yelled a voice. The horrible truth dawned on her.

"Let go of me!" she yelled, shaking violently. She broke free of the guard's grasp, and got up. However, it was to late. She was surrounded by seven guards, each pointing their halberds at her.

"Naughty, naughty slave. You aren't allowed to run away. I suppose I'll have to discipline you." said a posh voice from behind a guard. She recognised it instantly. It was that snobby, abusive, vile, disgusting, rotten, two-faced prince that she had to call a husband.

"Leave me alone! Can't you see? I. HATE. YOU." she yelled.

"But your so fun to play with." said the prince.

He snapped his fingers, and the guard moved to reveal him. He was wearing a red jumper, made out of rich velvet, with blue trousers, made of fine silk and various rubies embedded in the side. He had a blue cape on, and a navy shrug over his top. He had green hair tied back in a pony tail, and blue eyes. He wore various rings and bracelets on his hand, and a big, chunky gold necklace around his neck.

Sakura glared at him. Instantly, she sprinted at him and punched him across the face. The prince took a few steps back, clutching his jaw.

"Why you filthy rodent! I'll have you hanged for that!" yelled the prince. He snapped his fingers.

"Dispatch of her!" He barked at his guards.

The guards raised their weapons again, pointing them at Sakura. She realised what a mistake she had made, and clenched her fist.

"Fine, Kill me. Maybe I'll be happier that way." she said. Defeated.

The guards stepped back, and the lead guard took out a sword. He put it at her neck.

"Now, now. I wouldn't do that." said a voice from the trees. The voice belonged to Naruto, who leapt down from the trees. He got into a fighting posture.

"Go away kid, this has nothing to do with you." said a guard, going for a jab with his spear at Naruto. The blonde grabbed the spear, and twisted it, making the guard let go. He took the spear from him and kicked the guard in the helmet, making it fall of him.

"Why you…" the guard shouted, raising a fist to punch the blonde. Naruto caught the punch and deflected it away, and crouched down. He swept the guards feet from under him, making the guard fall. He leapt onto the body of the guard and jumped towards the others.

"Forget the girl! Get him!" yelled the leader.

Naruto parried a slash from a guard, then stabbed the guard with the spear. He let go of the now useless spear, and kicked another guard away, before pivoting around and punching another guard in the gut. He ducked under a jab from yet another guard, then leapt up, upper cutting the said guard. He span around, roundhouse kicking the fifth guard in the face. He leapt up and kicked the guard the three times in the face, then used the guard as leverage to leap off and punch the sixth guard hard. All of the lesser guards were now unconscious or dead. The lead guard glared at Naruto in anger.

"Fine then boy, you have some skill. Let's dance." he said, taking off his helmet. He removed his heavy armour, revealing a flexible black jumpsuit under. The guard rushed at Naruto with the sword he was going to kill Sakura with, and tried to decapitate him. Naruto ducked under the slice, and kicked the guard in the face with a powerful kick. He leapt up and then punched the guard in the gut, then span around, elbowing the guard away.

"No more Mr Nice Guy!" he yelled, rushing the blonde again. Naruto leapt over the guard, spinning around. However, the guard punched Naruto in the face as soon as he landed. He then punched him the gut, then landed an uppercut to the blonde's jaw. Naruto stumbled, but quickly recovered. He blocked a punch, then went to punch him in the gut, but the guard caught his punch. They were now holding each others fists, and struggled against the other trying to get free. Eventually, the guard won the struggle and punched Naruto hard in the gut. The blonde clutched his gut in pain.

"It's time for you to leave." he said, landing a 3 punch combo on the injured blonde. He then sent Naruto flying with a straight, powerful kick. The blonde hit a tree hard, and hit the floor, face first.

Sakura watched the entire thing, amazed. Her 'hero' was now apparently dead. The guard walked forward, picking up his sword. He crouched down beside the blonde.

"You shouldn't have picked a fight with me, kid. Now it's time you leave." he said, rearing to his full height. He raised the sword up, blade down, grasping the hilt with his hands. He brought the blade down into Naruto's back, the sword going straight through.

Sakura saw it. The blade went straight through, and she knew now it was over. She ran over to the guard.

"You…killed him…" she said, tears forming.

"And?" the guard said, pulling the blade out. It was coated with his blood.

"He did it for me…And I didn't even know him!" she cried out, holding her head in her hands.

The guard threw the sword away, and slapped Sakura.

"Shut up. Now, let's see what the prince wants to do with you." said the guard. He turned around, but was sent flying by a powerful punch. Sakura looked up and saw the blonde, still in the punch position.

"What…The sword…You…" she said, looking at him in awe. He smiled at her.

"It takes a lot more then some sword to kill me." he said, laughing.

His chest was still bleeding, but coated in some weird…red aura. It was healing rapidly.

"What is that?" Sakura asked, getting up. Her eyes never left the red aura.

"Oh, To be honest, I don't really know." he said, scratching the back of his head. However, he spun around suddenly. The guard let out a roar and charged Naruto. The blonde got into a fighting stance.

"You've troubled me enough." said the blonde.

He let out a breath-taking fast punch, smashing the guard in the face. He kicked the guard in the gut, then roundhouse kicked the guard to the floor. Just before the guard hit the floor, Naruto grabbed him by the cuff, and threw him forwards. He ran with the flying guard, and punched him in the gut. The guard hit the same tree Naruto hit, and hit the floor. Naruto picked up his own sword and stabbed through the guards' chest.

The blonde sighed.

The prince watched from far away. He ran away during the skirmish, and was way to far away for those…Rodents…to get him. He laughed to himself, and walked away, his cape flourishing.

_End Flashback_

Naruto walked with Sakura, arriving at a street. Sakura walked into a well-gardened home, and pulled out some keys. She opened the door, and walked inside. Naruto waved her goodbye, and she waved him back. She shut the door, and Naruto kept walking down the path, to his house.

Somewhere else, Agent Brown let out an evil laugh.

"Perfect!" he laughed, looking at his invention.


End file.
